Phase II development of an automated DNA sequence variation analysis software package is proposed. The software analyzes diploid DNA sequencing and mixed methylation analysis samples from phenotypically stratified patient groups. The software package detects essentially all mutations of any type, and then classifies and scores them. The goals of this Phase II are to improve upon the successful Phase I implementation and complete the originally proposed development plan. This includes automated interpretation of mutations and methylation state and association of detected mutations with a phenotypic group. PROPOSED COMMERCIAL APPLICATION: NOT AVAILABLE